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Also, the dungeons you may go to randomly in the middle of one can include Magnagate dungeons. I just entered one, not listed on the standard dungeon lists, which had Snivy in it so they aren't DLC exclusive. Will look into it and try to catalogue

Got Kyurem in the special missions. Heard through 2ch that B/W Kyurem are also battleable here. Gotta say, though, I hate that they have Dragon Tail. Massive pain in the butt...I run out of Revive Seeds so quickly

The evolutionary items are really limited to the Beartic minigame. There is confirmation that the Thunderstone has been found there, and since I have seen the Sun/Moon Hearts, it pretty much supports the claim. Seems like it will only be the reward at the 2500 point target though. These prizes reset everytime you finish a dungeon/mission/quest.

As for the evolve by happiness thing, the Pokemon must stay on your active team for some time (I evolved by Woobat simply by going through several very easy quests in and out, in and out. Takes about 6-7 dungeon missions to get it to enough happiness). When you check on your Pokemon's status screen (the second page), a faint line written in brown on the bottom will indicate that it is ready to evolve. This line happened in several circumstances which I tested:
1) If your Pokemon has levelled up beyond its evolution level but you choose to withhold its evolution
2) As in 'evolve by happiness' cases, when the happiness is achieved
3) In Piloswine's case, if it relearns Ancient Power, this line appears too, and it will evolve into Mamoswine when you level it up again

Have had some confirmation on the Kami Trio. Seems like they aren't mission based but are akin to how the random legends appear in previous series. Landorus is found on 8/F of Breezy Plains, but it's not a guarantee appearance (its name simply appears in the Pokemon that can appear list). I have encountered one but it didn't join me after I killed it.

As for the other two, it seems like we have to depend on the random warp thing of the dungeons. The Golden Chambers are back, and the higher the level of 'mystery' of the dungeon (as denoted by the numbers 1 to 5), the more likely you get warped to these 'map-less' dungeons. While the commoner place is the 'Mapless Street' where you can find the starters and Axew, occasionally you get warped to a Golden Chamber. Thundurus is found in the Golden Chamber accessed via the Iron Rust Mountain, and Tornadus is found in the Golden Chamber via the Large Glacier. Since the level of mystery is reset each time you finish a quest / dungeon, I think the easiest way to encounter these Golden Chambers is when these dungeons have Mystery 5. Again, it's random whether you go to the Mapless Street or the Golden Chamber, and despite their names present on the list, they may or may not appear again.